I feel firmly that the the "Neville's Heroes" subplot made up for any residual squickyness I felt about Snape pining for Lily.

I now have this great mental image of Filch wandering around Hogwarts going "I see nuuuting. I hear nuuuting." And maybe Snape in a monocle.

Neville becoming a semi-dashing badass covers a multitude of sins.